OBJECTIVE To map genomic diversity of Measles virus (MeV) isolates collected during 2009-2017 from ten states of India. METHODS Genome sequencing of Indian isolates and comparative genomics with global MeV using phylogeny, population stratification and selection pressure approaches were performed. RESULTS The first report of complete genome sequences of forty-three Indian MeV isolates belonging to genotypes D4 (eight) and D8 (thirty-five). Three Indian isolates mapped to named strains D4-Enfield, D8-Villupuram and D8-Victoria. Indian D4 isolates deviate from standard genome length due to indels in M-F intergenic region. Estimated nucleotide substitution rates of Indian MeV derived using genome and individual genes are lower than that of global isolates. Phylogeny revealed genotype-based temporal clustering, suggesting existence of two lineages of D4 and three lineages of D8 in India. Absence of spatial clustering suggests role of cross-border travel in MeV transmission. CONCLUSIONS Evolutionary analyses suggest the need for surveillance of MeV in India, particularly in view of diversified trajectories of D4 and D8 isolates. This study contributes to global measles epidemiology and indicates no major impact on antigenicity in Indian isolates, thereby substantiating the use of current vaccines to meet measles elimination target of 2023 set by World Health Organization for South-East Asia Region.

中文翻译：

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印度麻疹病毒多样性的特征：基因组测序和比较基因组学研究。

目的绘制2009-2017年间从印度十个州收集的麻疹病毒（MeV）分离株的基因组多样性图。方法采用系统发育，群体分层和选择压力方法，对印度分离株进行基因组测序，并利用全球MeV进行比较基因组学分析。结果首次报道了属于基因型D4（八）和D8（三十五）的43种印度MeV分离株的完整基因组序列。三个印度分离株映射到命名菌株D4-Enfield，D8-Villupuram和D8-Victoria。由于MF基因间区域存在插入缺失，印度D4分离株偏离标准基因组长度。使用基因组和单个基因估算的印度MeV核苷酸取代率估计低于全球分离株。系统发育揭示了基于基因型的时间聚类，提示在印度存在两个D4血统和三个D8血统。缺乏空间聚类表明跨界旅行在MeV传播中的作用。结论进化分析表明在印度需要监测MeV，特别是考虑到D4和D8分离株的轨迹多样化。这项研究有助于全球麻疹流行病学研究，并表明对印度分离株的抗原性没有重大影响，从而证实了当前疫苗的使用，可以达到世界卫生组织东南亚地区设定的2023年消灭麻疹的目标。特别是考虑到D4和D8分离株的多样化轨迹。这项研究有助于全球麻疹流行病学研究，并表明对印度分离株的抗原性没有重大影响，从而证实了当前疫苗的使用，可以达到世界卫生组织东南亚地区设定的2023年消灭麻疹的目标。特别是考虑到D4和D8分离株的多样化轨迹。这项研究有助于全球麻疹流行病学研究，并表明对印度分离株的抗原性没有重大影响，从而证实了当前疫苗的使用，可以达到世界卫生组织东南亚地区设定的2023年消灭麻疹的目标。